Complete Genome Assemblies of All Xanthomonas translucens Pathotype Strains Reveal Three Genetically Distinct Clades.

Florian Goettelmann,Claude Bragard,Jonathan M Jacobs,Ralf Koebnik,Roland Kölliker,Bruno Studer,Sébastien Cunnac,Veronica Roman-Reyna

doi:10.3389/fmicb.2021.817815

Abstract

The Xanthomonas translucens species comprises phytopathogenic bacteria that can cause serious damage to cereals and to forage grasses. So far, the genomic resources for X. translucens were limited, which hindered further understanding of the host–pathogen interactions at the molecular level and the development of disease-resistant cultivars. To this end, we complemented the available complete genome sequence of the X. translucens pv. translucens pathotype strain DSM 18974 by sequencing the genomes of all the other 10 X. translucens pathotype strains using PacBio long-read technology and assembled complete genome sequences. Phylogeny based on average nucleotide identity (ANI) revealed three distinct clades within the species, which we propose to classify as clades Xt-I, Xt-II, and Xt-III. In addition to 2,181 core X. translucens genes, a total of 190, 588, and 168 genes were found to be exclusive to each clade, respectively. Moreover, 29 non-transcription activator-like effector (TALE) and 21 TALE type III effector classes were found, and clade- or strain-specific effectors were identified. Further investigation of these genes could help to identify genes that are critically involved in pathogenicity and/or host adaptation, setting the grounds for the development of new resistant cultivars.

Highlights

Xanthomonas translucens is a species of Gram-negative phytopathogenic bacteria that causes serious damage in gramineous plants
We have identified a total of 13 type III non-transcription activator-like effector (TALE) effector classes that could constitute a core set of effectors in X. translucens
The TALEs identified in pv. cerealis strain CFBP 2541 correspond to the TALE previously identified in strain Nxtc01, with the TALE of class TalDP having a similar sequence to Nxtc01-Tal1 (Shah et al, 2019). As these four TALEs have previously been shown to have a role in virulence, the corresponding effectors we identified in this study could play a similar role in their respective strain (Falahi Charkhabi et al, 2017; Peng et al, 2019; Shah et al, 2019)

Summary

Introduction

Xanthomonas translucens is a species of Gram-negative phytopathogenic bacteria that causes serious damage in gramineous plants. Recent genome sequence data loosely supported this phenotypic classification (Peng et al, 2016; Hersemann et al, 2017; Langlois et al, 2017; Shah et al, 2021), these groups are not clearly defined based on the genetic relationships between the strains. Cerealis could be genetically distinct from the other “translucens” group pathovars (Bragard et al, 1997; Rademaker et al, 2006; Peng et al, 2016; Langlois et al, 2017). Xanthomonas strains causing dieback in pistachio (Pistacia vera L.) were found to belong to the X. translucens species, a species so far thought to infect only monocotyledonous plants (Giblot-Ducray et al, 2009). The group A strain was found to be closely related to pathovars translucens, secalis, and undulosa, while the group B strain was closest to pv. cerealis, suggesting that the ability to infect pistachio may have evolved two separate times in X. translucens

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Conclusion